PDB-9dve: X-ray crystal structure of Kohinoor reversibly switchable fluores...

ID or keywords:

Entry

Database: PDB / ID: 9dve

Title

X-ray crystal structure of Kohinoor reversibly switchable fluorescent protein

Components

Kohinoor

Keywords

FLUORESCENT PROTEIN / switchable / beta barrel

Function / homology

DI(HYDROXYETHYL)ETHER

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Richardson, B.C. / He, Y. / Iuliano, J.N. / Woroniecka, H.A. / French, J.B.

Funding support

United States, 3items

Organization	Grant number	Country
National Science Foundation (NSF, United States)	2042704	United States
Department of Energy (DOE, United States)	KP1605010	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	P30GM133893	United States

Citation

Journal: Chem Sci / Year: 2025
Title: Ultrafast photophysics of a positive reversibly switchable fluorescent protein.
Authors: Fatima, A. / He, Y. / Iuliano, J.N. / Greetham, G.M. / Malakar, P. / Hall, C. / Woroniecka, H.A. / Richardson, B.C. / French, J.B. / Lukacs, A. / Tonge, P.J. / Meech, S.R.

History

Deposition	Oct 7, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 3, 2025	Provider: repository / Type: Initial release
Revision 1.1	Sep 10, 2025	Group: Database references / Category: citation / citation_author Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Oct 1, 2025	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9dve.cif.gz	465.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9dve.ent.gz	389.4 KB	Display	PDB format
PDBx/mmJSON format	9dve.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dv/9dve ftp://data.pdbj.org/pub/pdb/validation_reports/dv/9dve	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Kohinoor

B: Kohinoor

C: Kohinoor

D: Kohinoor

hetero molecules

104 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Kohinoor

hetero molecules

defined by author&software
Evidence: gel filtration
26.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Kohinoor

defined by author&software
26 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Kohinoor

defined by author&software
26 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Kohinoor

defined by author&software
26 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	138.530, 73.628, 93.219
Angle α, β, γ (deg.)	90.00, 115.86, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Kohinoor Mass: 26001.447 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.08 Å³/Da / Density % sol: 40.93 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: .12-.14M magnesium nitrate hexahydrate 18-24% PEG-3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9792 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 23, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.15→83.89 Å / Num. obs: 44302 / % possible obs: 96 % / Redundancy: 2.9 % / CC_1/2: 0.995 / R_merge(I) obs: 0.072 / R_pim(I) all: 0.05 / R_rim(I) all: 0.088 / Net I/σ(I): 8 / Num. measured all: 128853
Reflection shell	Resolution: 2.15→2.21 Å / % possible obs: 90.4 % / Redundancy: 2.9 % / R_merge(I) obs: 0.697 / Num. measured all: 9850 / Num. unique obs: 3406 / CC_1/2: 0.796 / R_pim(I) all: 0.492 / R_rim(I) all: 0.857 / Net I/σ(I) obs: 1.5

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
Aimless		data scaling
XDS		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.15→83.89 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 0.32 / Phase error: 35.63 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.272	2210	4.99 %
R_work	0.244	-	-
obs	0.246	44297	95.7 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.15→83.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6379	0	7	156	6542

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	6544
X-RAY DIFFRACTION	f_angle_d	1.104	8860
X-RAY DIFFRACTION	f_dihedral_angle_d	13.183	2300
X-RAY DIFFRACTION	f_chiral_restr	0.052	925
X-RAY DIFFRACTION	f_plane_restr	0.005	1156

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.15-2.19	0.4252	123	0.3741	2406	X-RAY DIFFRACTION	88
2.19-2.24	0.4083	148	0.355	2653	X-RAY DIFFRACTION	96
2.24-2.3	0.3793	126	0.3445	2595	X-RAY DIFFRACTION	95
2.3-2.36	0.3749	118	0.3457	2587	X-RAY DIFFRACTION	94
2.36-2.43	0.3838	143	0.3438	2606	X-RAY DIFFRACTION	96
2.43-2.51	0.3863	138	0.3651	2624	X-RAY DIFFRACTION	96
2.51-2.6	0.3811	127	0.3289	2657	X-RAY DIFFRACTION	96
2.6-2.7	0.2937	130	0.2852	2598	X-RAY DIFFRACTION	94
2.7-2.83	0.3132	147	0.2656	2639	X-RAY DIFFRACTION	97
2.83-2.98	0.3343	140	0.2743	2677	X-RAY DIFFRACTION	98
2.98-3.16	0.3034	133	0.2783	2702	X-RAY DIFFRACTION	98
3.16-3.41	0.3291	133	0.2423	2711	X-RAY DIFFRACTION	97
3.41-3.75	0.2482	142	0.221	2646	X-RAY DIFFRACTION	97
3.75-4.29	0.233	131	0.2069	2614	X-RAY DIFFRACTION	95
4.29-5.41	0.2018	161	0.1787	2694	X-RAY DIFFRACTION	98
5.41-83.89	0.2391	170	0.2335	2678	X-RAY DIFFRACTION	95

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	8.2	-3.76	-2.8496	3.3474	3.5547	3.8505	0.1081	-0.5062	-0.0999	-0.5744	0.0857	0.5518	0.0162	-0.2988	-0.1201	0.273	-0.0189	-0.0252	0.4877	0.0421	0.3752	-13.014	24.933	33.484
2	4.6278	-0.9391	-0.6056	2.8641	-0.8915	3.7098	0.2626	-0.2245	0.2251	0.3164	-0.1995	0.4382	-0.18	-0.2357	-0.0465	0.2969	-0.0136	0.0299	0.367	-0.0426	0.3344	-8.577	25.256	37.833
3	1.87	-0.0212	-0.4143	2.9957	-0.7076	3.0997	0.1618	-0.0494	0.1838	0.1284	-0.0223	0.4988	-0.0967	0.0111	-0.1355	0.3153	-0.0097	-0.0089	0.3994	-0.0339	0.4477	-2.764	28.772	29.257
4	3.6934	-3.2954	3.2676	7.6028	-4.0342	3.791	-0.2189	-0.2769	-0.0931	0.5855	-0.3246	-0.8442	-0.5059	-0.5019	0.3456	0.577	-0.0667	-0.0091	0.7543	-0.0374	0.5332	9.791	26.659	38.944
5	4.9844	2.9414	-1.5268	6.1797	-1.5552	9.064	0.4467	0.2947	0.9582	-1.0749	-0.0474	1.1024	-0.1044	-0.5448	-0.5068	0.4262	0.0491	-0.0119	0.392	-0.0215	0.7441	-4.249	36.446	19.787
6	3.4167	3.7477	-3.7209	7.2315	-5.1335	7.1151	0.4515	-0.6063	0.3248	0.8034	-0.4291	0.3813	-0.5413	0.6395	-0.0986	0.381	-0.044	0.0187	0.5311	-0.0684	0.5473	-3.979	31.49	41.177
7	5.7864	-5.6987	0.1605	8.8202	-0.7454	1.8658	0.15	0.6775	0.3521	0.7134	-0.4065	-0.4001	-0.4155	0.8218	0.3082	0.378	-0.0795	-0.0041	1.0849	-0.0686	0.4297	28.843	42.84	2.424
8	2.7036	-2.7938	-0.2679	5.2698	0.2916	1.1413	-0.0468	0.4249	0.141	-0.202	-0.0202	-0.3971	0.0999	1.0278	0.0214	0.3923	-0.1096	0.0015	1.1589	0.0485	0.4445	27.287	37.82	-0.808
9	1.6136	0.2397	0.3398	2.7661	-0.501	2.5143	0.0217	0.4295	0.1136	0.0951	0.0774	-0.2424	-0.2247	0.6657	-0.0934	0.3373	-0.0976	0.0147	0.6517	-0.002	0.2957	19.771	37.424	6.995
10	2.599	2.5218	-0.2085	4.5218	5.0113	9.8836	-0.1815	0.3745	0.0045	-0.1132	0.7864	-0.2405	0.4591	1.133	-0.5402	0.3726	0.1019	-0.0696	0.7903	-0.0217	0.4324	15.809	27.188	4.623
11	3.463	-1.0164	-1.965	1.6072	-0.5965	2.8813	-0.0615	1.042	-0.0828	-0.0049	0.0231	-0.1954	0.0339	0.6506	0.1083	0.3403	-0.1329	-0.0358	0.8264	0.0052	0.4415	18.9	39.171	1.214
12	4.9012	4.4604	-6.3664	3.8945	-5.4105	7.5565	0.2972	0.8254	-0.829	0.1066	0.1464	0.1537	0.6007	-1.4014	-0.6823	0.855	-0.0226	-0.2493	1.1799	0.08	0.9327	4.723	39.231	1.971
13	6.8082	-5.3197	3.2454	8.9778	-5.6811	5.9534	-0.2777	0.3872	0.2821	0.3033	-0.3067	-0.9093	0.0483	0.2926	0.5843	0.3397	-0.016	-0.006	0.4257	-0.1443	0.428	42.826	25.852	27.744
14	2.2317	0.3505	-0.9717	6.2707	-2.1166	4.5576	-0.2995	-0.0895	-0.3465	-0.4503	0.063	-0.5614	0.3575	0.0642	0.2537	0.2714	-0.0282	0.0382	0.4723	-0.0973	0.4254	38.085	22.028	28.042
15	9.0177	-2.0812	-0.4691	4.3848	-1.1034	3.5185	-0.0792	0.1005	-0.2964	0.0564	0.1032	-0.0178	0.1036	-0.3083	0.0075	0.3269	-0.0931	-0.0289	0.4053	-0.0694	0.2943	33.476	26.516	21.691
16	2.3907	-2.983	-1.7078	7.0795	4.1281	5.1234	-0.1147	0.3866	-0.3228	-0.7987	-0.0774	0.2604	-0.0295	-0.7863	0.3826	0.6667	-0.1764	-0.002	0.691	-0.106	0.4892	26	19.744	27.558
17	4.253	-0.8054	-2.3364	0.4768	-0.815	3.0775	-0.8698	0.421	-1.032	0.7153	-0.0544	0.8404	1.3022	-0.6431	0.9249	0.7029	-0.1831	0.1551	0.6999	-0.2276	0.7118	29.162	15.784	23.806
18	4.653	0.2883	-0.8052	5.5076	-1.6761	4.073	-0.1163	-0.1082	-0.4494	0.43	0.0671	-0.565	0.1854	-0.1484	0.08	0.3884	-0.0026	-0.0032	0.57	-0.1085	0.452	35.368	24.978	36.276
19	1.9831	-1.7782	-0.9976	7.0888	1.2616	0.3503	-0.593	0.0636	-0.693	-0.8693	0.0688	-0.1982	1.6913	-0.0263	0.3841	1.6213	0.0753	0.2231	0.4681	0.0786	0.7374	-3.035	0.408	16.169
20	3.2288	1.2184	-2.6215	6.9242	-1.9923	2.4826	-1.7368	0.0275	0.0363	-0.6246	0.9383	-0.3813	2.3065	-0.192	0.2333	1.3232	0.1049	0.1301	0.4404	-0.049	0.4849	-0.744	6.374	14.349
21	1.5192	-1.878	-0.1202	1.5964	-0.6033	-0.1335	-1.0554	-0.6213	-0.6261	1.5026	0.8086	0.0825	0.5232	0.099	0.3316	1.4983	0.4317	0.1764	0.8002	0.1005	0.6566	6.245	2.158	24.105
22	5.0547	-0.7409	-3.0876	3.2152	0.1119	8.6872	-0.2426	-0.3187	0.1817	0.3433	0.3339	-0.2532	0.7073	0.3232	-0.1298	0.4509	0.0197	-0.1226	0.2773	-0.0223	0.3781	2.04	15.881	12.295
23	0.862	1.0807	1.2276	3.2057	-2.5703	8.4156	-0.3744	-0.1063	-0.5396	0.8617	0.0271	-0.0178	-0.2342	1.4594	0.5367	0.8857	0.5259	-0.032	0.591	-0.0071	0.4678	14.44	8.292	18.246
24	1.4094	0.4653	-0.3247	0.9745	-0.9505	2.5969	-0.707	-0.4817	-0.4352	-0.3852	0.1592	0.1974	1.9792	0.409	0.277	1.5243	0.3123	0.0985	0.6586	0.0653	0.5902	7.112	4.762	12.139

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 6:24 )	A	6 - 24
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 25:70 )	A	25 - 70
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 71:159 )	A	71 - 159
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 160:175 )	A	160 - 175
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 176:192 )	A	176 - 192
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 193:221 )	A	193 - 221
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 6:24 )	B	6 - 24
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 25:69 )	B	25 - 69
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 70:157 )	B	70 - 157
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 158:180 )	B	158 - 180
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 181:213 )	B	181 - 213
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 214:224 )	B	214 - 224
13	X-RAY DIFFRACTION	13	( CHAIN C AND RESID 6:40 )	C	6 - 40
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 41:86 )	C	41 - 86
15	X-RAY DIFFRACTION	15	( CHAIN C AND RESID 87:135 )	C	87 - 135
16	X-RAY DIFFRACTION	16	( CHAIN C AND RESID 136:166 )	C	136 - 166
17	X-RAY DIFFRACTION	17	( CHAIN C AND RESID 167:193 )	C	167 - 193
18	X-RAY DIFFRACTION	18	( CHAIN C AND RESID 194:220 )	C	194 - 220
19	X-RAY DIFFRACTION	19	( CHAIN D AND RESID 9:47 )	D	9 - 47
20	X-RAY DIFFRACTION	20	( CHAIN D AND RESID 48:71 )	D	48 - 71
21	X-RAY DIFFRACTION	21	( CHAIN D AND RESID 73:120 )	D	73 - 120
22	X-RAY DIFFRACTION	22	( CHAIN D AND RESID 121:147 )	D	121 - 147
23	X-RAY DIFFRACTION	23	( CHAIN D AND RESID 148:166 )	D	148 - 166
24	X-RAY DIFFRACTION	24	( CHAIN D AND RESID 167:220 )	D	167 - 220

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